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- PDB-5oj7: Sirtuin 4 orthologue from Xenopus Tropicalis in complex with ADP-... -

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Basic information

Entry
Database: PDB / ID: 5oj7
TitleSirtuin 4 orthologue from Xenopus Tropicalis in complex with ADP-ribose
ComponentsNAD-dependent protein deacylase
KeywordsHYDROLASE / Sirt4 Deacylase Posttranslational modification
Function / homology
Function and homology information


Regulation of pyruvate dehydrogenase (PDH) complex / Transcriptional activation of mitochondrial biogenesis / histone H3K14 deacetylase activity, NAD-dependent / histone H3K9 deacetylase activity, NAD-dependent / histone H4K16 deacetylase activity, NAD-dependent / histone H3K18 deacetylase activity, NAD-dependent / histone H3K56 deacetylase activity, NAD-dependent / histone H3K4 deacetylase activity, NAD-dependent / NAD+ binding / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups ...Regulation of pyruvate dehydrogenase (PDH) complex / Transcriptional activation of mitochondrial biogenesis / histone H3K14 deacetylase activity, NAD-dependent / histone H3K9 deacetylase activity, NAD-dependent / histone H4K16 deacetylase activity, NAD-dependent / histone H3K18 deacetylase activity, NAD-dependent / histone H3K56 deacetylase activity, NAD-dependent / histone H3K4 deacetylase activity, NAD-dependent / NAD+ binding / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / mitochondrial matrix / zinc ion binding
Similarity search - Function
Sirtuin, class II / Sirtuin, catalytic core small domain superfamily / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / DHS-like NAD/FAD-binding domain superfamily
Similarity search - Domain/homology
Chem-AR6 / NAD-dependent protein deacylase
Similarity search - Component
Biological speciesXenopus tropicalis (tropical clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsPannek, M. / Steegborn, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
Oberfrankenstiftung Germany
CitationJournal: Nat Commun / Year: 2017
Title: Crystal structures of the mitochondrial deacylase Sirtuin 4 reveal isoform-specific acyl recognition and regulation features.
Authors: Pannek, M. / Simic, Z. / Fuszard, M. / Meleshin, M. / Rotili, D. / Mai, A. / Schutkowski, M. / Steegborn, C.
History
DepositionJul 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 2.0Jan 17, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _chem_comp.pdbx_synonyms ..._atom_site.occupancy / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD-dependent protein deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0658
Polymers32,1001
Non-polymers9657
Water4,702261
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration, Single, monomeric gelfiltration peak
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint8 kcal/mol
Surface area13230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.390, 74.660, 109.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-730-

HOH

21A-734-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein NAD-dependent protein deacylase / Regulatory protein SIR2 homolog


Mass: 32100.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus tropicalis (tropical clawed frog)
Gene: sirt4, TGas015j14.1-001 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): CodonPlus
References: UniProt: Q28CB4, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides

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Non-polymers , 5 types, 268 molecules

#2: Chemical ChemComp-AR6 / [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE / Adenosine-5-Diphosphoribose


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.6 % / Description: Diamond-shape
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M BICINE pH 8.0 17% PEG6000 / PH range: 7.8-8.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.911656 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 2, 2015 / Details: MIRROR
RadiationMonochromator: SI111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.911656 Å / Relative weight: 1
ReflectionResolution: 1.58→20 Å / Num. obs: 39280 / % possible obs: 99.8 % / Redundancy: 5.1 % / CC1/2: 1 / Rrim(I) all: 0.036 / Net I/σ(I): 23.7
Reflection shellResolution: 1.58→1.62 Å / Redundancy: 5.2 % / Num. unique obs: 2868 / CC1/2: 0.7 / Rrim(I) all: 0.853 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XSCALEdata scaling
PHASER2.5.6.phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TWI

4twi


Resolution: 1.58→19.73 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.969 / SU B: 3.184 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18648 1964 5 %RANDOM
Rwork0.1524 ---
obs0.15411 37316 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.097 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å2-0 Å2
2--0.66 Å2-0 Å2
3----0.35 Å2
Refinement stepCycle: 1 / Resolution: 1.58→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2257 0 59 261 2577
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0192410
X-RAY DIFFRACTIONr_bond_other_d0.0020.022243
X-RAY DIFFRACTIONr_angle_refined_deg2.6081.9583279
X-RAY DIFFRACTIONr_angle_other_deg1.2893.0025153
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6575299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.19723.391115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.9915382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8381519
X-RAY DIFFRACTIONr_chiral_restr0.170.2355
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0212748
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02598
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3192.4791160
X-RAY DIFFRACTIONr_mcbond_other2.3112.4781159
X-RAY DIFFRACTIONr_mcangle_it3.3513.7041453
X-RAY DIFFRACTIONr_mcangle_other3.3523.7051454
X-RAY DIFFRACTIONr_scbond_it3.572.9251249
X-RAY DIFFRACTIONr_scbond_other3.5692.9251249
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3034.2241821
X-RAY DIFFRACTIONr_long_range_B_refined7.15821.5042867
X-RAY DIFFRACTIONr_long_range_B_other7.15821.5042867
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.58→1.621 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 142 -
Rwork0.267 2705 -
obs--99.75 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.53180.17490.32320.25950.12020.5315-0.0141-0.0006-0.0502-0.0077-0.0225-0.0226-0.0117-0.00440.03650.0018-0.00480.00040.02350.00250.018823.158515.188740.0645
200000000000000-00.0902-0.0695-0.08540.05370.06590.080941.372131.952947.1162
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 315
2X-RAY DIFFRACTION2C1

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